Vortigaunts

Zombine

Zombines are Alyx's nickname for Combine soldiers who have been attacked by headcrabs, and thus, transformed into zombies.

Combine-based zombies are known to attack with merciless abandon, by activating and holding onto a grenade, while running toward the player.

Dr. Breen

At the end of Half-Life 2 Breen was heard at the end of a conversation with a Combine Advisor. In Episode One, you see the recording of this conversation, in which it is revealed he was talked into participating/using a host body for the Combine. After this, a sort of pod appears and lets loose a sort of psychic blast (manifested to the player as a violent red throb and noise) that is visibly painful for Alyx.

The Citadel

The Citadel will explode at the end of Episode One but it seems that isn't the direct result of the actions of Freeman. It seems that the energy reactor of the Citadel was unstable and so deactivated all Combine teleports and communication-devices. The explosion of the Citadel was meant to send a message to the Combine. The content of this message is unknown in Episode One but luckily Alyx managed to make a copy of it. It is clear that the Combine are trying to take control again, after Breen disappeared.